Merge branch 'open-atmos:main' into asian-option

.github/workflows/pdoc.yml

@@ -0,0 +1,49 @@
+name: pdoc
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: '0 13 * * 4'
+
+jobs:
+  pdoc:
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+    runs-on: ${{ matrix.platform }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          persist-credentials: false
+      - uses: actions/setup-python@v5.2.0
+        with:
+          python-version: 3.9
+      - env:
+          JUPYTER_PLATFORM_DIRS: 1
+        run: |
+          pip3 install pdoc nbformat
+          pip install -e . -e ./examples
+
+          python - <<EOF
+          import glob, nbformat
+          for notebook_path in glob.glob('examples/PyMPDATA_examples/*/*.ipynb'):
+            with open(notebook_path, encoding="utf8") as fin:
+              with open(notebook_path + ".badges.md", 'w') as fout:
+                fout.write(nbformat.read(fin, nbformat.NO_CONVERT).cells[0].source)
+          EOF
+
+          PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html PyMPDATA examples/PyMPDATA_examples -t docs/templates --math
+      - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}
+        uses: JamesIves/github-pages-deploy-action@4.1.1
+        with:
+          branch: pdoc
+          folder: html
+          clean: true

.github/workflows/projects.yml

@@ -0,0 +1,19 @@
+name: Add new issues and pull requests to project board
+
+on:
+  issues:
+    types:
+      - opened
+  pull_request_target:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add to project
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/add-to-project@v1.0.2
+        with:
+          project-url: https://github.com/orgs/open-atmos/projects/6
+          github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}

.github/workflows/pypi.yml

@@ -0,0 +1,57 @@
+name: pypi
+
+defaults:
+  run:
+    shell: bash
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+    - cron: '0 13 * * 4'
+  release:
+    types: [published]
+
+jobs:
+  dist:
+    strategy:
+      matrix:
+        package-dir: [".", "examples"]
+      fail-fast: false
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
+      - uses: actions/setup-python@v5.2.0
+        with:
+          python-version: "3.10"
+
+      - run: pip install twine build
+
+      - run: |
+          unset CI
+          cd ${{ matrix.package-dir }}
+          python -m build 2>&1 | tee build.log
+          exit `fgrep -v "warning: no previously-included files matching" buid.log | fgrep -i warning | wc -l`
+          twine check --strict dist/*
+          exit `tar tzf dist/*.tar.gz | fgrep ".ipynb" | wc -l`
+          cd ..
+
+      - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: pypa/gh-action-pypi-publish@release/v1.12
+        with:
+          attestations: false
+          repository_url: https://test.pypi.org/legacy/
+          packages-dir: ${{ matrix.package-dir }}/dist
+
+      - if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1.12
+        with:
+          attestations: false
+          packages-dir: ${{ matrix.package-dir }}/dist

.github/workflows/tests+pypi.yml → .github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: tests+pypi
+name: tests
 
 defaults:
   run:
@@ -11,8 +11,6 @@ on:
     branches: [ main ]
   schedule:
     - cron: '0 13 * * 4'
-  release:
-    types: [published]
 
 jobs:
   precommit:
@@ -21,44 +19,20 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v5.2.0
         with:
-          python-version: "3.10" 
+          python-version: "3.10"
       - run: |
           pip install pre-commit
           pre-commit clean
           pre-commit autoupdate
           pre-commit run --all-files
 
-  nojit_and_codecov:
-    runs-on: ubuntu-latest
-    env:
-      NUMBA_DISABLE_JIT: 1
-    steps:
-    - uses: actions/checkout@master
-      with:
-        submodules: recursive
-        fetch-depth: 0 
-    - uses: actions/setup-python@v5.2.0
-      with:
-        python-version: 3.9
-    - name: Generate coverage report
-      run: |
-        pip install -e .[tests] -e ./examples
-        pip install pytest-cov
-        pytest --durations=10 -We tests/unit_tests --cov-report=xml --cov=PyMPDATA
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        fail_ci_if_error: true
-        verbose: true
-
   pylint:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
       with:
         submodules: recursive
-        fetch-depth: 0 
+        fetch-depth: 0
     - name: Set up Python 3.9
       uses: actions/setup-python@v5.2.0
       with:
@@ -79,53 +53,57 @@ jobs:
         # TODO #299
         nbqa pylint --disable=fixme,trailing-whitespace,wrong-import-position,wrong-import-order,ungrouped-imports \
                     --disable=duplicate-code,invalid-name,missing-module-docstring,line-too-long,missing-function-docstring,redefined-outer-name,too-many-arguments,no-member,too-many-locals,cell-var-from-loop,missing-class-docstring $(git ls-files '*.ipynb')
-  pdoc:
-    strategy:
-      matrix:
-        platform: [ubuntu-latest, macos-latest, windows-latest]
-    runs-on: ${{ matrix.platform }}
+
+  zenodo_json:
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
+      - uses: notiz-dev/github-action-json-property@release
+        with:
+          path: '.zenodo.json'
+          prop_path: 'creators'
+
+  devops:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
+      - run: pip install -r tests/devops_tests/requirements.txt
+      - run: pip install -e . -e ./examples
+      - env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: pytest --durations=10 -v -s -We -p no:unraisableexception -k "not run_notebooks" tests/devops_tests
+
+  nojit_and_codecov:
+    needs: [ precommit, pylint, zenodo_json, devops ]
+    runs-on: ubuntu-latest
+    env:
+      NUMBA_DISABLE_JIT: 1
+    steps:
+      - uses: actions/checkout@master
         with:
           submodules: recursive
-          persist-credentials: false
+          fetch-depth: 0
       - uses: actions/setup-python@v5.2.0
         with:
           python-version: 3.9
-      - env:
-          JUPYTER_PLATFORM_DIRS: 1
+      - name: Generate coverage report
         run: |
-          pip3 install pdoc nbformat
-          pip install -e . -e ./examples
-
-          python - <<EOF
-          import glob, nbformat
-          for notebook_path in glob.glob('examples/PyMPDATA_examples/*/*.ipynb'):
-            with open(notebook_path, encoding="utf8") as fin:
-              with open(notebook_path + ".badges.md", 'w') as fout:
-                fout.write(nbformat.read(fin, nbformat.NO_CONVERT).cells[0].source)
-          EOF
-
-          PDOC_ALLOW_EXEC=1 python -We -m pdoc -o html PyMPDATA examples/PyMPDATA_examples -t docs/templates --math
-      - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}
-        uses: JamesIves/github-pages-deploy-action@4.1.1
+          pip install -e .[tests] -e ./examples
+          pip install pytest-cov
+          pytest --durations=10 -We tests/unit_tests --cov-report=xml --cov=PyMPDATA
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
         with:
-          BRANCH: pdoc
-          FOLDER: html
-          CLEAN: true
-
-  zenodo_json:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: notiz-dev/github-action-json-property@release
-        with: 
-          path: '.zenodo.json'
-          prop_path: 'creators'
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          verbose: true
 
   tests:
     timeout-minutes: 120
-    needs: [nojit_and_codecov, pylint, pdoc, precommit, zenodo_json]
+    needs: [nojit_and_codecov]
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
@@ -138,7 +116,7 @@ jobs:
       - uses: actions/checkout@v2
         with:
           submodules: recursive
-          fetch-depth: 0 
+          fetch-depth: 0
 
       - uses: actions/setup-python@v5.2.0
         with:
@@ -152,7 +130,7 @@ jobs:
       # https://github.com/numba/numba/issues/6350#issuecomment-728174860
       - if: startsWith(matrix.platform, 'ubuntu-')
         run: echo NUMBA_THREADING_LAYER=omp >> $GITHUB_ENV
-        
+
       - env:
           NUMBA_OPT: 1
         run: |
@@ -165,7 +143,7 @@ jobs:
           python -m pytest --durations=10 -p no:unraisableexception -We -k "test_timing_3d" tests/smoke_tests
 
   examples:
-    needs: [pylint, precommit]
+    needs: [nojit_and_codecov]
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
@@ -217,7 +195,7 @@ jobs:
       #   uses: mxschmitt/action-tmate@v3
       #   with:
       #     limit-access-to-actor: true
-  
+
       - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12'}}
         uses: eine/tip@master
         with:
@@ -226,58 +204,3 @@ jobs:
             /github/home/figures/*.svg
             /github/home/figures/*.gif
 
-  devops:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          submodules: recursive
-          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
-      - run: pip install -r tests/devops_tests/requirements.txt
-      - run: pip install -e . -e ./examples
-      - env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: pytest --durations=10 -v -s -We -p no:unraisableexception -k "not run_notebooks" tests/devops_tests
-
-  dist:
-    strategy:
-      matrix:
-        package-dir: [".", "examples"]
-      fail-fast: false
-    runs-on: ubuntu-latest
-    needs: [tests, examples, devops]
-    permissions:
-      id-token: write
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          submodules: recursive
-          fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
-      - uses: actions/setup-python@v5.2.0
-        with:
-          python-version: "3.10"
-
-      - run: pip install twine build
-
-      - run: |
-          unset CI
-          cd ${{ matrix.package-dir }}
-          python -m build 2>&1 | tee build.log
-          exit `fgrep -v "warning: no previously-included files matching" buid.log | fgrep -i warning | wc -l`
-          twine check --strict dist/*
-          exit `tar tzf dist/*.tar.gz | fgrep ".ipynb" | wc -l`
-          cd ..
-
-      - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: pypa/gh-action-pypi-publish@release/v1.12
-        with:
-          attestations: false
-          repository_url: https://test.pypi.org/legacy/
-          packages-dir: ${{ matrix.package-dir }}/dist
-
-      - if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@release/v1.12
-        with:
-          attestations: false
-          packages-dir: ${{ matrix.package-dir }}/dist
-

README.md

@@ -15,7 +15,7 @@
 [![PL Funding](https://img.shields.io/static/v1?label=PL%20Funding%20by&color=d21132&message=NCN&logoWidth=25&logo=image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABQAAAANCAYAAACpUE5eAAAABmJLR0QA/wD/AP+gvaeTAAAAKUlEQVQ4jWP8////fwYqAiZqGjZqIHUAy4dJS6lqIOMdEZvRZDPcDQQAb3cIaY1Sbi4AAAAASUVORK5CYII=)](https://www.ncn.gov.pl/?language=en)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
 
-[![Github Actions Build Status](https://github.com/open-atmos/PyMPDATA/actions/workflows/tests+pypi.yml/badge.svg?branch=main)](https://github.com/open-atmos/PyMPDATA/actions)
+[![Github Actions Build Status](https://github.com/open-atmos/PyMPDATA/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/open-atmos/PyMPDATA/actions)
 [![Appveyor Build status](http://ci.appveyor.com/api/projects/status/github/open-atmos/PyMPDATA?branch=main&svg=true)](https://ci.appveyor.com/project/slayoo/pympdata/branch/main)
 [![Coverage Status](https://codecov.io/gh/open-atmos/PyMPDATA/branch/main/graph/badge.svg)](https://app.codecov.io/gh/open-atmos/PyMPDATA)